jLM.Solvers.ConstBoundaryConc Class Reference

Public Member Functions
	__init__ (self, lmFile, exact=False)
	setBoundary (self, species, concs, boundary)
	hookSimulation (self, t, lattice)

Public Attributes
	exact = exact
	rdme = lmFile
list	dists = []
	distTable = None
	bMask = np.zeros_like(self.rdme.siteLattice)
	bLattice = np.zeros_like(self.rdme.siteLattice)

Detailed Description

Solver with fixed concentration boundary conditions

The simulation hook runs a cythonized function which destructively sets
the specified boundaries to a prescribed concentration. 

Constructor & Destructor Documentation

__init__()

jLM.Solvers.ConstBoundaryConc.__init__	(		self,
			lmFile,
			exact = False )

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Member Function Documentation

hookSimulation()

jLM.Solvers.ConstBoundaryConc.hookSimulation	(		self,
			t,
			lattice )

Replaces all particles on boundary according to B.C.s

setBoundary()

jLM.Solvers.ConstBoundaryConc.setBoundary	(		self,
			species,
			concs,
			boundary )

Specify boundary conditions

    Specify a boundary condition using a species (or list of species), a 
    concentration (or list of concentrations; in mol/L), and a specification 
    of the boundary in terms of a binary lattice. Subsequent calls will add 
    new boundary conditions.  When the boundary region given by a subsequent 
    call overlaps with a previously described region, the later call will 
    override the earlier conditions.

    Args:
        species (:py:class:`~jLM.Types.Species`):
            Species at boundary
        concs (float):
            Concentrations
        boundary (:py:class:`~numpy.ndarray`):
            Binary lattice describing the boundary

Member Data Documentation

bLattice

jLM.Solvers.ConstBoundaryConc.bLattice = np.zeros_like(self.rdme.siteLattice)

bMask

jLM.Solvers.ConstBoundaryConc.bMask = np.zeros_like(self.rdme.siteLattice)

dists

list jLM.Solvers.ConstBoundaryConc.dists = []

distTable

jLM.Solvers.ConstBoundaryConc.distTable = None

exact

jLM.Solvers.ConstBoundaryConc.exact = exact

rdme

jLM.Solvers.ConstBoundaryConc.rdme = lmFile

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The documentation for this class was generated from the following file:

• /data2/LM_zls_github/Lattice-Microbes/src/jlm/jLM/Solvers.py